Enigma Revolution
by Kira31
Summary: A different galaxy, one with the Human Systems Alliance as a vassal under the Turian Hierarchy. A different Cerberus, one more focused on releasing Humanity from their chains. A different Shepard, one who uses his tragedy to motivate himself in a new direction. As tensions rise to a boiling point, how will the galaxy react to a revolution caused by a faceless man, an Enigma.


**Warning: The following has scenes of extreme violence that may be unsuitable for some readers. Reader discretion is advised**

 **Mindoir, Outskirts of the Therum settlement, Human Systems Alliance, January 6th 2170 C.E.**

Mindoir, one of humanities relatively few colonies in the Attican Traverse, and one of the even fewer garden worlds humanity had. After the Tragedy of Shanxi during the Relay 314 incident where a Turian diplomatic vessel carrying diplomats from the Citadel Council was shot down by the Alliance fleet that had recently liberated the planet from a Turian blockade, the Turian Hierarchy were able to convince the Council to declare a sanctioned military venture to secure a full surrender from the Alliance at any cost. Eventually the Alliance accepted a full and unconditional surrender after a Turian blockade of the Sol system and the assassination of the Alliance Prime minister, with the terms of the peace being very harsh on humanity.

Firstly the Alliance would accept full blame for the war, and pay reparations to the families of the Citadel soldiers who had died in the conflict, they also had to petition the Council for the right to colonize any new planets in the Attican Traverse, or anywhere outside the sector of space allotted to them as the Earth Systems Alliance Space. Perhaps the most humiliating part of the peace was that the Alliance would become a client state under the Turian Hierarchy, being required to pay a tribute of one-tenth of their overall earnings to their overlords, have Turian military figures watch over all Alliance military training, and to cut their military spending by one-tenth.

All of these factors led to Humanity slowly expanding under these new rules instead of the comparatively rapid expansion before the Relay 314 incident. With a significantly lower economic base to go off, and a reduced fleet to care for, until recently the Alliance had only maintained two or three colonies in the Attican Traverse. Now however, they had managed to use various bribes and political favors to get the right to colonize nine new worlds in the Traverse, and while many species were wary of allowing such a explosion of human population, mainly the Batarians who had become used to the slowly expanding ways of the Alliance giving them time to claim the Traverse themselves, but eventually the Council was won over.

That led to a scene where a teenage boy was currently fixing the program the farm used to operate the automated sowing vehicles, which they desperately needed for the upcoming planting season. Leaning back on his chair Jack Shepard looked out the window to his right, seeing the bustling city of Therum in the distance cursing his luck that the program his mother had bought had a glitch, rendering the system unusable until Jack fixed it. If he had his way, he would be in the city with his sister right now, celebrating the last festival before planting season started.

'Of course,' Jack thought grimly with a smirk on his face, watching as his new algorithm was being tested in the system 'there's another reason we always have a festival on this day, at least for the adults there is.' While to outside observers Mindoir was just a normal farming colony, it was an open secret in the Alliance that the population of the colony was mainly Alliance Navy veterans, mostly from the Relay 314 incident that were either dismissed because of injuries during the conflict, or from the budget cuts after peace was signed. Many higher ups in the Alliance Parliament made sure this would happen as a way of paying back those who were hurt by the conflict and aftermath of the conflict.

Jack himself had lost his father during a Council fleet breaking through the defensive blockade the Alliance had around Shanxi, and after his mother had been dismissed from the Alliance his family had lived with his grandmother on Luna, until now that is. While it had taken Jack a while to become accustomed to the planets larger gravity and the farm life in general, he had grown fond of it, unlike his sister Jane, who never got used to the the static nature of everything here, his mother joked that Jane had inherited her space faring nature.

The reason why many of the vets celebrated on this day every year, also lay with the reason why tensions were always high on the colony, with the large amounts of colonies, the Alliance found their fleets and marines were unable to protect them, and thus had requested from their overlords the Turians to lease marines and ships to protect the outer colonies, which Mindoir was one of. The Turian marines were obviously not liked by the adults in the colonies, and as such every year when the old garrison left and the new one arrived, there was always a one day in between where there were no Turian guards, and that left the colony to it's own devices, and as such the colonist celebrated as much as they could before the Turians returned.

Seeing the system working as intended now, Jack allowed himself a smile of pride, before checking his watch he decided that he would go into the city and enjoy as much of the festival as he could. As Jack rode his bike along the dirt road, he was momentarily deafened as a large group of ships flew by, heading straight to the city. 'Strange,' he mused as his eyes followed the ships 'those don't have Turian, or Alliance markings, and Mr. O'Reily said they weren't able to do the air show this year...' Jacks thoughts trailed off as he watched in shock as the ships simultaneously fired on the city, fires erupting in their wakes, before they stopped and hovered over certain areas of the city.

After breaking out of his shock Jack began to pedal faster than he ever had before, desperate to make it to the city, and his family as fast as he could. Every second that passed seemed like an eternity for Jack, as hundreds of questions filled his head, who were these people? Why were they here? What were they here for? As these questions and more pounded around in the young mans head, he finally made it into the city proper, and after ditching his bike, the crowded streets would be hard enough to move through without the vehicle.

After running through countless streets, and finding the result of what these attackers obviously did to those who couldn't out run them, Jack came across the market square, and a sight that chilled his very bones. The center of the square was cleared of all stands and stalls from the festival, in their place was one of the attackers ships, standing around the square was a group that Jack had only seen in vids, Batarians. There were at least twenty just in this one square, most facing in toward the center of the square, but Jack was able to get a good look at those who were watching for external threats, with their multiple sets of eyes, seemingly perpetual sneers as they looked at the human colony with unveiled disgust. However, it was when Jack decided to see what the guards facing inward were guarding that his blood froze in his veins.

Kneeling in front of the ship, groups being led into it as he stared, were many colonists, some that Jack knew closely, being herded where ever the Batarians wanted like cattle. Most of the colonists were children, few of them over eighteen, and a few of the newer colonists, it seemed to Jack that with how many veterans there were, they had taken death over enslavement. Not seeing his sister or his mother, Jack decided to move on in his search, sending a prayer to whoever would listen for the poor unfortunate souls in front of him. Jack had almost turned away, when he began to hear a child's wail, coming from a baby that couldn't be over six months. One of the guards barked at the girl holding the baby speaking in a language neither could understand, before the guard having apparently lost his patience took out his handgun and fired a few shots into both the baby, and the girl, both of them falling back with a muted thump.

For a moment, Jack sat there, numbed by what he had just seen, before the world became tinted in pure crimson, felt the blood rushing in his ears, and seeing his hands shake right in front of him. Looking around frantically he managed to grab the first weapon he could find, an old first contact era sniper rifle. Trying to steady his shaking hands Jack lined up a shot on the Batarian that did the deed, before pulling the trigger and hearing the gun bark out, although unprepared for the recoil, Jack had been able to hit the slaver by pure luck. His luck however, quickly ran out when the other slavers noticed Jacks position and opened fire on him. Jack swiftly turned and ran around the side of a building, attempting to fire on the rest of the slavers, but was never able to pop out for more than a few seconds before having to turn back or become Swiss cheese. After one attempt to take a shot rewarded him with a retorting shot to the arm, Jack held the gun in the crook of his arm and ran deeper into the city, hoping some of the children were able to run away, Batarians chasing after him firing shots at his retreating form.

* * *

Jack Harper was not a happy man.

Harper had recently relocated to Mindoir in an effort to lay low and avoid Turian and, by extension, Alliance attempts to figure out his identity and bring him to "justice", but he had been prepared for that. After starting Cerberus, Harper's attempt to ensure that Humanity was at the top of the galactic pyramid, they needed to be at the top, it might be the only chance the galaxy would have.

But instead of the peaceful idyllic colony he had hoped to spend a few months on after the newest witch hunt had started, he had instead witnessed the attack on the colonies largest city only a week after he had arrived. He muttered a curse at his luck as he pulled the last of the foliage off of his transport ship. After looking around and not seeing any immediate danger, Harper pulled out a carton of cigarettes and lit one up, grimacing with displeasure and wishing he had brought a cigar from his hideout. As he let out a puff of smoke, Harper looked on with a frown as he watched the formally peaceful colony burn, while he did not know who had raided the planet, Harper did not particularly care one way or the other. From what he had seen of the ships, they were alien, and that was all the information he needed, and seeing this happen strengthened his belief for the necessity of Cerberus. The other races were obviously terrified of Humanities potential, and were taking steps to curtail any advancement they could.

Harper jolted in surprise when he saw a figure running toward him, being chased by four others. Pulling out a old earth pair of binoculars, Harper got a better look at who these people were. The one leading the pack was a boy, likely one of the colonials, with a rifle held under his arm, behind him were four aliens, Batarians if Jack remembered correctly. The boy had sweat dripping down his face and blood falling from his arm, while the Batarians chased at a steady pace with grins on their faces, obviously taking some form of amusement with their improvised "hunt". The boy had obviously seen Jack, as he had started to speed up slightly and head directly to Jack, while the boy's hunters had yet to spot him in the underbrush.

As Jack put the binoculars down, Jack rubbed his eyes in frustration, he knew what he should do, get in the transport and go, leaving the boy to his unfortunate and undeserved fate. It may be callous, but he was the head of an underground organization spanning all of human space, he was the center point of Cerberus, with only himself knowing the meaning behind many of the operations and experiments done. But at the same time, seeing that boy running, the desperate hope that was on his face as he noticed Jack staring back at him, wanting only to escape from the veritable monsters chasing after him, reminded Jack of his time on Shanxi, of the Turian bombardment of entire city blocks whenever they so much as saw a soldier uniform.

Grunting as he came to a conclusion, Jack dropped and stomped out his cigarette as he pulled out his pistol and let it charge up, "After all," he muttered as he took aim at one of the Batarians, "If I can't even save one kid, what was the point of making Cerberus?" With that, he fired off a quick burst at the alien, grimacing when he saw the telltale blue flicker of shields pop up. Jack quickly started to lay a covering fire for the boy, who took this chance to drop the rifle, put his head down, and book it for Jack and his shuttle, using the trees on the forest edge to dodge the return fire.

When the boy was finally close enough, Jack called him over and shouted at him to get in, still firing on the approaching Batarians, grinning when he finally broke through one's shields and nicking him on the left side of his face. Hearing the boy open the shuttle door and get in, Jack prepared to fire one last burst and make a run for it, when he was taken aback as he felt his body jerk backwards, pain blooming in his chest. As he stumbled back, coughing up a glob of blood into his hand, he cursed his luck, pressing himself against the side of the transport as he stumbled inside. He could feel himself bleeding out, his gaze growing blacker and blacker as he slowly made his way to the cockpit, ignoring the wide-eyed look the boy gave him. As he entered the cockpit, he put in the coordinates for his final backup base, finishing his task he left the ship on autopilot and slowly slid down the console, leaving a red trail behind him. Turning himself so he was facing the boy, he managed a rueful smile and held his hand out and said in a hoarse whisper "Name's...Jack...who're...who're you kid?"

The boy stared in shock for a moment before realizing the man in front of him was on his last few second of life. Gaining a determined look on his face, the boy took the older mans hand and said in a voice that sounded close to cracking with each syllable "My...My name's Jack too." He gave a soft, sad smile as he spoke for the man who gave his life for him.

Harper barked a short laugh that turned into a coughing fit, and managed to work out "Irony...huh?...Guess a Jack...was supposed to die today...Listen kid, trust...Cer..ber...us..." With those last words out, Harper felt the last of his resolve fall away as he drifted into the abyss, managing to turn his head to stare out the side window, looking as the planet's atmosphere faded away to the stars of the galaxy. If he could say any other words, he would have said there was no better way to go out.

* * *

 **Hidden Cerberus Base, Uncharted System, January 19th 2170 C.E.**

Jack Shepard jolted upright as he awoke, the blaring of the alarm clock he had programmed ending the nightmare he had suffered through the entire night long. Rubbing his eyes to rid himself of the last of the sleep he felt, he swung his legs over the edge of the bed, and moved to the facilities washroom to clean and change. These last few days at the facility had certainly been hectic, for the first four days Jack had been unable to even fall asleep for fear that the Batarian's had followed him. And because of the chemical makeup of the planet's atmosphere he couldn't even walk outside without an environment proof suit and air tank, something that the base had few of. The base did have enough air, food, and water stocks to last only himself for another month, as the base's V.I. system felt the need to remind him every day, but they could only be replenished via outside sources.

While it had only taken him two days to figure out how to work the base's communication array, he had to keep his sleepless self occupied somehow after all, he had been hesitant to use it, first because of his paranoia of the Batarian's watching for any communication to find him, and then because he noticed how there was only one destination for the communication to go out to, and it was labeled "Full Operative Conference". He assumed that these operatives were part of Cerberus, and this conference would be seen by them as their leader calling on them.

Yes, Jack had learned all about Cerberus since arriving here, thanks to a series of holo-messages left here by the leader, the same man who saved him on Mindoir, Jack Harper. It seems this base was to be revealed to his successor when he chose one, and contained messages explaining many of Cerberus' inner workings, who his operatives were and what they were in charge of, and one message that was the last one Jack had seen, one that chilled him to the bone.

Pushing the thought of the last message out of his mind, Jack slipped on the baggy clothes that lined the closet, and took a deep breath of confidence, he had decided to send the call out today, before he had simply planned to try and learn how the transport he had arrived here worked and leave a beacon on for the Alliance to find. But, after hearing the last message...he had changed his mind, what he had heard, the thoughts it had put in his head, he wanted, no he **needed** to try and continue what Harper had started, not just for Humanity, but for the whole galaxy. Like it or not, the galaxy needed Cerberus, and Cerberus needed to know what to do.

Sitting down in front of the communication interface, he quickly altered the settings, changing his young, teenage voice to sound much older to give the illusion that Harper was still alive. As he sent the call out, Jack rested his head on one hand, with a grim look on his face, and decided to begin his changes to Cerberus as soon as he stabilized the internal situation, after all, they would need as many allies as they could get before he initiated Operation: New Dawn.

* * *

Authors note: Alright! So there we go, first chapter in my newest story! I hope you all enjoyed it, I've had this idea floating around in my head for a while and I've just recently put it down on paper, so to speak. I have to say, this is probably one of the most gruesome scenes I've written, so much so that I will probably put this down as either M, or at least T, and maybe even put a warning at the start of the chapter, but I'll leave that to future me. Hope you all enjoyed, and thank you in advance to anyone who reviews, favorites, or alerts this story! And to all you wonderful people who have read this, I wish you all a good day/night/evening/whereever you are!


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